# List of top-scoring protein chains for t2k-100-30-str2 hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.cse.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1nfjA 89 2.74e-21 1h0xA 100 2.48e-20 d.68.6.1 76451 1nh9A 87 3.32e-20 1udvA 89 1.62e-10 1r7aA 504 9.55e-02 1ml8A 134 1.39e-01 d.227.1.2 85013 1fbaA 361 2.59e-01 1fbaA c.1.10.1 29120 1olsB 342 3.25e-01 1v1rB 342 3.29e-01 1fnmA 691 3.43e-01 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1rlkA 117 4.24e-01 1j5xA 342 5.24e-01 c.80.1.1 71591 1p1lA 102 5.99e-01 d.58.5.2 87695 2pia 321 6.02e-01 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1hzpA 335 6.37e-01 1hn9A c.95.1.1 61455 c.95.1.1 61456 1i50K 120 6.41e-01 d.74.3.2 61765 1cliA 345 6.83e-01 1cliA d.79.4.1 39816 d.139.1.1 41459 1k4nA 192 7.28e-01 d.32.1.5 72059 1dtwB 342 7.37e-01 1qs0B c.36.1.7 31828 c.48.1.2 33102 1j5rA 371 8.16e-01 1p42A 270 8.61e-01 d.14.1.7 87754 d.14.1.7 87755 1nzjA 298 8.68e-01 1kzhA 555 1.01e+00 c.89.1.1 73361 1hq3B 126 1.04e+00 1aoiD a.22.1.1 16444 1jmkC 230 1.09e+00 c.69.1.22 71747 1seiA 130 1.19e+00 1seiA d.140.1.1 41463 1ukuA 102 1.25e+00 1pbn 289 1.27e+00 1b8oA c.56.2.1 33771 1px5A 349 1.43e+00 1cf2O 337 1.53e+00 1b7gO c.2.1.3 29994 d.81.1.1 39909 1wba 175 1.56e+00 1wba b.42.4.1 25591 1nijA 318 1.63e+00 c.37.1.10 85741 d.237.1.1 85742 1gln 468 1.67e+00 1gln a.97.1.1 18752 c.26.1.1 31588 1kr4A 125 1.81e+00 d.58.5.2 72889 1vhwA 253 1.86e+00 1b7gO 340 1.90e+00 1b7gO c.2.1.3 29992 d.81.1.1 39907 1oi2A 366 1.96e+00 c.32.1.2 87039 d.79.2.2 87040 1draA 159 2.06e+00 1vdrA c.71.1.1 34831 1nslA 184 2.11e+00 d.108.1.1 86137 1o2dA 371 2.11e+00 e.22.1.2 86591 1fmaE 150 2.15e+00 1fmaE d.41.5.1 38630 1m3uA 264 2.17e+00 c.1.12.8 84784 1b8oA 284 2.30e+00 1b8oA c.56.2.1 33762 1jubA 311 2.32e+00 1odkA 235 2.36e+00 c.56.2.1 86863 1aky 221 2.55e+00 1zin c.37.1.1 31896 g.41.2.1 45197 1bpyA 335 2.79e+00 1bpyA a.60.6.1 17980 a.60.12.1 75819 d.218.1.2 75820 1h1wA 289 2.87e+00 d.144.1.7 83460 1dtdA 303 2.98e+00 1aye c.56.5.1 33823 1fm0E 150 3.32e+00 1fmaE d.41.5.1 38629 1j09A 468 3.90e+00 a.97.1.1 77025 c.26.1.1 77026 1qgdA 662 4.01e+00 c.36.1.6 88367 c.36.1.10 88368 c.48.1.1 88369 1bq3B 246 4.15e+00 1qhfA c.60.1.1 33979 1rztA 331 4.17e+00 2dorA 311 4.28e+00 2dorA c.1.4.1 28593 1hyeA 313 4.35e+00 2cmd c.2.1.5 61400 d.162.1.1 61401 1qgoA 264 4.39e+00 1qgoA c.92.1.2 35596 3pnp 289 4.43e+00 1b8oA c.56.2.1 33763 1aye 401 4.54e+00 1aye c.56.5.1 33824 d.58.3.1 39065 1bn6A 294 4.54e+00 1bn6A c.69.1.8 34678 1e58A 249 4.55e+00 1qhfA c.60.1.1 59262 1rkuA 206 4.57e+00 1hu4A 288 4.70e+00 1hu4A 1n5dA 288 4.70e+00 c.2.1.2 80030 1g59A 468 4.71e+00 a.97.1.1 60257 c.26.1.1 60258 1gokA 303 4.78e+00 c.1.8.3 65420 1k6aA 303 4.78e+00 c.1.8.3 72081 1fxmA 302 4.91e+00 1taxA 1g5hA 454 5.16e+00 1g5hA c.51.1.1 60270 d.104.1.1 60271 1epxA 370 5.45e+00 1fbaA c.1.10.1 29150 1lct 333 5.69e+00 1cb6A c.94.1.2 35836 1kmiZ 214 5.70e+00 h.4.11.1 72752 1nulA 152 5.70e+00 1nulA c.61.1.1 34011 1i1gA 141 5.81e+00 a.4.5.32 65982 d.58.4.2 65983 1uu3A 310 5.98e+00 1bn7A 294 6.10e+00 1bn6A c.69.1.8 34677 2bopA 85 6.13e+00 2bopA d.58.8.1 39217 1cm7A 363 6.15e+00 1cnzA c.77.1.1 35063 1j1yA 136 6.22e+00 1ftrA 296 6.28e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 1j27A 102 6.50e+00 1rpl 251 6.79e+00 1bpyA a.60.12.1 75933 d.218.1.2 75934 2frvA 264 6.82e+00 2frvA e.19.1.1 43303 1cqwA 295 6.88e+00 1b6g c.69.1.8 34679 1i1wA 303 6.97e+00 c.1.8.3 76732 1cb6A 691 7.17e+00 1cb6A c.94.1.2 35840 c.94.1.2 35841 1qhfA 240 7.19e+00 1qhfA c.60.1.1 33960 1bpb 248 7.20e+00 1bpyA a.60.12.1 75811 d.218.1.2 75812 1ir6A 424 7.30e+00 c.107.1.2 71342 1pswA 348 7.73e+00 c.87.1.7 88287 2hfh 109 7.91e+00 2hfh a.4.5.14 16145 1f7uA 607 8.12e+00 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 4pfk 319 8.14e+00 3pfk c.89.1.1 35582 1sphA 88 8.29e+00 1ptf d.94.1.1 40544 1jm6A 407 8.31e+00 a.29.5.1 66876 d.122.1.4 66877 1v54E 109 8.31e+00 1jysA 242 8.34e+00 c.56.2.1 77216 1vgyA 393 8.43e+00 2occE 109 8.60e+00 2occE a.118.11.1 19224 1auoA 218 8.70e+00 1auoA c.69.1.14 34716 1aurA 218 8.76e+00 1auoA c.69.1.14 34718 1dorA 311 8.94e+00 2dorA c.1.4.1 28595 1ctf 74 8.96e+00 1ctf d.45.1.1 38759 1gveA 327 9.09e+00 c.1.7.1 70597 1q8rA 120 9.15e+00 1m5yA 408 9.34e+00 a.167.1.1 78664 d.26.1.1 78665 d.26.1.1 78666 6pfkA 319 9.35e+00 3pfk c.89.1.1 35583 1mxa 383 9.46e+00 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1fi2A 201 9.61e+00 1fi2A b.82.1.2 59845 1o66A 275 9.84e+00 1kamA 194 9.87e+00 c.26.1.3 72254 1rg9A 383 9.99e+00 1iz7A 295 1.02e+01 c.69.1.8 76982 1bs2A 607 1.02e+01 1bs2A a.27.1.1 16930 c.26.1.1 31597 d.67.2.1 39563 1cv2A 296 1.03e+01 1bn6A c.69.1.8 34680 1cz3A 168 1.06e+01 1d1gA c.71.1.1 34891 1mb4A 370 1.07e+01 c.2.1.3 78908 d.81.1.1 78909 1lxnA 99 1.09e+01 d.58.48.1 84737 1h6hA 143 1.09e+01 d.189.1.1 65681 1je5A 206 1.09e+01 1je5A b.40.4.7 62909 3pfk 319 1.10e+01 3pfk c.89.1.1 35581 1qm4A 396 1.13e+01 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1d4oA 184 1.14e+01 1d4oA c.31.1.4 31748 1pch 88 1.19e+01 1ptf d.94.1.1 40564 1d1gA 168 1.19e+01 1d1gA c.71.1.1 34889 1m8aA 70 1.24e+01 d.9.1.1 74579 3pgm 241 1.25e+01 1qhfA c.60.1.1 33982 1eqtA 68 1.26e+01 1b3aA d.9.1.1 37412 1jykA 254 1.27e+01 c.68.1.13 67458 1feuA 206 1.33e+01 1feuA b.53.1.1 59801 1b3aA 67 1.34e+01 1b3aA d.9.1.1 37410 1b31A 302 1.40e+01 1taxA c.1.8.3 28892 1krhA 338 1.41e+01 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1bg4 302 1.45e+01 1taxA c.1.8.3 28806 1k2xA 177 1.47e+01 1k3fA 253 1.48e+01 c.56.2.1 68105 1e3tA 203 1.52e+01 1d4oA c.31.1.4 31749 1pil 112 1.52e+01 2pii d.58.5.1 39072 1ra9 159 1.52e+01 1vdrA c.71.1.1 34820 1q8bA 105 1.55e+01 1rxyA 253 1.56e+01 1nxcA 478 1.58e+01 3mhtA 327 1.58e+01 6mhtA c.66.1.26 34234 1hgxA 183 1.62e+01 1tc1A c.61.1.1 34027 1gy8A 397 1.64e+01 c.2.1.2 83376 1k6xA 352 1.67e+01 c.2.1.2 68238 1oi7A 288 1.70e+01 c.2.1.8 87049 c.23.4.1 87050 1mku 123 1.71e+01 1poa a.133.1.2 19590 1qahA 136 1.71e+01 1ptmA 329 1.76e+01 1bu5A 147 1.77e+01 5nul c.23.5.1 31155 1jd1A 129 1.79e+01 1qu9A d.79.1.1 62890 1j1qA 261 1.82e+01 1uqrA 154 1.83e+01 1kexA 155 1.84e+01 b.18.1.2 77350 1f4pA 147 1.87e+01 5nul c.23.5.1 59651 1k6iA 352 1.89e+01 c.2.1.2 68223 1ik6A 369 1.90e+01 c.36.1.7 66174 c.48.1.2 66175 1adoA 363 1.92e+01 1fbaA c.1.10.1 29124 1v04A 355 1.92e+01 1trb 320 1.92e+01 1trb c.3.1.5 30529 c.3.1.5 30530 1mxb 383 1.94e+01 1mxb d.130.1.1 41329 d.130.1.1 41330 d.130.1.1 41331 1lylA 504 1.94e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 2bby 69 1.96e+01 2bby a.4.5.15 16148 1humA 69 1.96e+01 1b3aA d.9.1.1 37397 1a8s 273 1.98e+01 1brt c.69.1.12 34710 1httA 423 2.01e+01 1adjA c.51.1.1 33178 d.104.1.1 40727 1kx5D 125 2.04e+01 a.22.1.1 77596 1un8A 552 2.09e+01 1brmA 367 2.11e+01 1brmA c.2.1.3 30030 d.81.1.1 39945 2pii 112 2.15e+01 2pii d.58.5.1 39071 1gxlA 213 2.15e+01 d.215.1.1 70713 6dfr 159 2.16e+01 1vdrA c.71.1.1 34874 1uv7A 110 2.17e+01 1h4vB 421 2.17e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1nom 248 2.18e+01 1bpyA a.60.12.1 75929 d.218.1.2 75930 1ne2A 200 2.19e+01 c.66.1.32 85586 1v2bA 177 2.22e+01 1bby 69 2.23e+01 2bby a.4.5.15 16149 1aoiD 99 2.25e+01 1aoiD a.22.1.1 16452 1lvwA 295 2.27e+01 c.68.1.6 84723 1eysL 280 2.28e+01 6prcL f.26.1.1 43515 1vk6A 269 2.31e+01 1j9lA 247 2.32e+01 c.106.1.1 62762 1mbxC 106 2.44e+01 d.45.1.2 78929 1ej2A 181 2.46e+01 1f9aA c.26.1.3 59414 1qayA 428 2.47e+01 1qaxA d.58.20.1 39378 d.179.1.1 42599 1adjA 421 2.47e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1e15A 499 2.47e+01 1e15A b.72.2.1 27810 c.1.8.5 29006 d.26.3.1 38440 1mj5A 302 2.48e+01 1clxA 347 2.50e+01 1taxA c.1.8.3 28899 1dysA 348 2.52e+01 1bvwA c.6.1.1 30669 1oxkB 134 2.52e+01 1une 123 2.53e+01 1poa a.133.1.2 19583 1kyqA 274 2.55e+01 c.2.1.11 73281 e.37.1.1 73282 1qo2A 241 2.60e+01 1qo2A c.1.2.1 28533 1g4iA 123 2.61e+01 1poa a.133.1.2 60241 1bu8A 452 2.61e+01 1gpl b.12.1.2 23647 c.69.1.19 34795 1dmaA 214 2.62e+01 1aerA d.166.1.1 42251 1g1eB 89 2.63e+01 1g1eB a.59.1.1 17931 1nkxA 348 2.64e+01 4bp2 130 2.65e+01 1poa a.133.1.2 19584 1f9aA 168 2.66e+01 1f9aA c.26.1.3 31602 1aoeA 192 2.68e+01 1aoeA c.71.1.1 34923 1o65A 246 2.69e+01 1jlnA 297 2.70e+01 1pty c.45.1.2 63172 1ebuA 358 2.70e+01 1ebuA c.2.1.3 30035 d.81.1.2 39950 1cs1C 386 2.72e+01 1ibjA c.67.1.3 34401 1l9wA 252 2.73e+01 c.1.10.1 84570 1cs1A 386 2.74e+01 1ibjA c.67.1.3 34399 1nwaA 203 2.80e+01 d.58.28.1 86295 1mgtA 174 2.81e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1h0cA 392 2.82e+01 c.67.1.3 83424 1lxjA 104 2.82e+01 d.58.48.1 84736 1ayyA 151 2.84e+01 1apyA d.153.1.5 42016 1pwhA 327 2.85e+01 1j9eA 147 2.94e+01 c.23.5.1 62756 1rpmA 278 2.94e+01 2shpA c.45.1.2 32679 1ebfA 358 2.96e+01 1ebuA c.2.1.3 30033 d.81.1.2 39948 1exmA 405 2.97e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1q5yA 85 2.98e+01 1nu0A 138 3.02e+01 1goiA 499 3.06e+01 b.72.2.1 65413 c.1.8.5 65414 d.26.3.1 65415 1lx7A 253 3.06e+01 c.56.2.1 74329 1ep2B 261 3.09e+01 1ep2B b.43.4.2 25666 c.25.1.3 31556 1gqnA 252 3.17e+01 1dckA 126 3.18e+01 1dbwA c.23.1.1 31097 1j9jA 247 3.19e+01 c.106.1.1 62758 1m7gA 211 3.30e+01 c.37.1.4 78724 1cmbA 104 3.31e+01 1cmbA a.43.1.2 17460 1mhdA 132 3.31e+01 1mhdA d.164.1.1 42175 1e1oA 504 3.32e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1gxjA 186 3.37e+01 d.215.1.1 70707 1hv9A 456 3.40e+01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1hkhA 279 3.42e+01 1spuB 727 3.43e+01 1oacA b.30.2.1 24399 d.17.2.1 38025 d.17.2.1 38026 d.82.1.1 40012 1gvnB 287 3.44e+01 c.37.1.21 76354 1jem 87 3.44e+01 1ptf d.94.1.1 40548 1gqoN 143 3.46e+01 c.23.13.1 76308 1cnzA 363 3.46e+01 1cnzA c.77.1.1 35061 1iugA 352 3.46e+01 1ib8A 164 3.47e+01 b.38.2.1 71168 d.52.4.1 71169 1gqoI 143 3.47e+01 c.23.13.1 76303 1gqoO 143 3.48e+01 c.23.13.1 76309 1gr0A 367 3.52e+01 c.2.1.3 70379 d.81.1.3 70380 1gxyA 226 3.53e+01 d.166.1.3 76380 1gqoY 143 3.53e+01 c.23.13.1 76318 1rowA 109 3.54e+01 1jqeA 292 3.55e+01 c.66.1.19 71789 1g0oA 283 3.61e+01 1ybvA c.2.1.2 60181 1a8o 70 3.69e+01 1a8o a.28.3.1 16953 1mdbA 539 3.71e+01 e.23.1.1 79008 1ndh 272 3.71e+01 1ndh b.43.4.2 25662 c.25.1.1 31552 1qycA 308 3.72e+01 1m5sA 297 3.72e+01 d.58.33.1 74511 d.58.33.1 74512 1opjA 293 3.75e+01 d.144.1.7 87230 1am3 70 3.78e+01 1kmmA 424 3.79e+01 1adjA c.51.1.1 33174 d.104.1.1 40723 1mzjA 339 3.79e+01 c.95.1.1 79700 c.95.1.1 79701 1ybvA 283 3.80e+01 1ybvA c.2.1.2 29948 1cmcA 104 3.83e+01 1cmbA a.43.1.2 17462 1gqoK 143 3.85e+01 c.23.13.1 76305 1gqoF 143 3.85e+01 c.23.13.1 76300 1ooeA 236 3.88e+01 c.2.1.2 87196 1gqoH 143 3.91e+01 c.23.13.1 76302 1gqoP 143 3.91e+01 c.23.13.1 76310 1gqoB 143 3.91e+01 c.23.13.1 76296 2cblA 305 3.93e+01 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1gqoR 143 3.93e+01 c.23.13.1 76312 1elkA 157 3.96e+01 1dvpA a.118.9.2 19217 1bg0 356 3.97e+01 1qh4A a.83.1.1 18476 d.128.1.2 41211 1crwG 333 3.99e+01 1dssG c.2.1.3 30026 d.81.1.1 39941